MEDIPS

DOI:10.18129/B9.bioc.MEDIPS

DNA IP-seq data analysis

Bioconductor version: Release (3.6)

MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.

Author: Lukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez Moyado

Maintainer: Lukas Chavez

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported source("//www.anjoumacpherson.com/biocLite.R") biocLite("MEDIPS")

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("MEDIPS")

PDF	R Script	MEDIPS
PDF		Reference Manual

Details

biocViews	ChIPSeq,CopyNumberVariation,Coverage,CpGIsland,DNAMethylation,DifferentialExpression,Genetics,GenomeAnnotation,Microarray,Preprocessing,QualityControl,SequenceMatching,Sequencing,Software,Visualization
Version	1.30.0
In Bioconductor since	BioC 2.7 (R-2.12) (7.5 years)
License	GPL (>=2)
Depends	R (>= 3.0),BSgenome,Rsamtools
Imports	GenomicRanges,Biostrings, graphics,gtools,IRanges, methods, stats, utils,edgeR,DNAcopy,biomaRt,rtracklayer,preprocessCore
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19,MEDIPSData,BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Source Package	MEDIPS_1.30.0.tar.gz
Windows Binary	MEDIPS_1.30.0.zip
Mac OS X 10.11 (El Capitan)	MEDIPS_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MEDIPS
Package Short Url	//www.anjoumacpherson.com/packages/MEDIPS/
Package Downloads Report	Download Stats